Simple Boolean Logic/Formatting Question

This has to be something simple, but I am new to Java and still learning, I've made it this far without having to ask a personal question but it's got me stumped.

I have three boxes, when they collide with my bullet the boolean should switch to false, when all three boxes have switched their assigned boolean to false the player should be taken to the game over screen. With Debug.Log I am able to see it's reading them as false, but it isn't switching them over in the inspector. So I feel like I might be instantly setting it back somehow. Here is all of my code for this particular script.

Edit:I should have clarified, updating the original post. It is attached to the prefab that is my bullet. So, all of these happen when my bullet experiences a collision. There is only one script.

 static var Counter : int = 0;
 var object : GameObject;
 var success : AudioClip;
 var thud : AudioClip;
 var explosion : GameObject;
 var fail : AudioClip;
 var boxhit1 : boolean = true;
 var boxhit2 : boolean = true;
 var boxhit3 : boolean = true; 
 
     
 function OnCollisionEnter (theCollision : Collision){
 
     if(theCollision.rigidbody){
     Instantiate(explosion, transform.position, transform.rotation);
     AudioSource.PlayClipAtPoint(fail, Camera.main.transform.position);
     Destroy(object);
     }
     
     else if(theCollision.gameObject.name == ("Box1") && boxhit1){
     theCollision.gameObject.AddComponent(Rigidbody);
     gameObject.Find("Box1").renderer.material.color = Color.black;
     Instantiate(explosion, transform.position, transform.rotation);
     AudioSource.PlayClipAtPoint(success, Camera.main.transform.position);
     Counter++;
     boxhit1=!boxhit1;
     Debug.Log("Box Hit 1: " + boxhit1);
     Destroy(object);
     }
     
     else if(theCollision.gameObject.name == ("Box2") && boxhit2){
     theCollision.gameObject.AddComponent(Rigidbody);
     gameObject.Find("Box2").renderer.material.color = Color.black;
     Instantiate(explosion, transform.position, transform.rotation);
     AudioSource.PlayClipAtPoint(success, Camera.main.transform.position);
     Counter++;
     boxhit2 = false;
     Debug.Log("Box Hit 2: " + boxhit2);
     Destroy(object);
     }
     
     else if(theCollision.gameObject.name == ("Box3") && boxhit3){
     theCollision.gameObject.AddComponent(Rigidbody);
     gameObject.Find("Box3").renderer.material.color = Color.black;
     Instantiate(explosion, transform.position, transform.rotation);
     AudioSource.PlayClipAtPoint(success, Camera.main.transform.position);
     Counter++;
     boxhit3 = false;
     Debug.Log("Box Hit 3: " + boxhit3);
     Destroy(object);
     }
     
     else if(theCollision.gameObject){
     Instantiate(explosion, transform.position, transform.rotation);
     AudioSource.PlayClipAtPoint(thud, transform.position);
     Destroy(object);
     }
     }
 
 function Update(){
 
 if(!boxhit1 && !boxhit2 && !boxhit3){
     Debug.Log("All are false!");
     Application.LoadLevel("GameOver"); 
     }
 }